From Protege Wiki
Double-clicking on OWL files
For all operating systems except OS X, Protege 4 works with double-click as installed - you simply follow the usual OS specific steps for indicating which application to use to open an OWL file. In the case of OS X there is an extra adjustment that needs to be done (we are working on removing this extra step).
If you are trying to enable double-click on an OS X machine, follow the instructions from editing the Info.plist to open the Info.plist file with a text editor. Add the following lines underneath any other key/value pair:
<key>CFBundleDocumentTypes</key> <array> <dict> <key>CFBundleTypeExtensions</key> <array> <string>owl</string> </array> <key>CFBundleTypeName</key> <string>OWL Ontology</string> <key>CFBundleTypeRole</key> <string>Viewer</string> </dict> </array>
Now configure double-click as you would with any other OS X application.
Thanks are due to Alan Ruttenberg for his suggestion on how to enable double-click on the OS X platform.